Paul de Vries described the difference between “methodological naturalism,” which is a disciplinary method that says nothing about God’s existence, from “metaphysical naturalism,” which “denies the existence of a transcendent God.” [Paul de Vries, “Naturalism in the Natural Sciences,” Christian Scholar’s Review 15(1986): 388–96]. The method of naturalism assumes that for everything we experience there is a natural explanation, whereas metaphysical naturalism is a worldview that denies the supernatural realm exists. [For discussions of this see Alvin Plantinga’s essay “Methodological Naturalism?” parts 1 and 2, which can be found at www.arn.org, and in the journal Perspectives on Science and Christian Faith (49 [1997]). Barbara Forrest’s “Methodological Naturalism and Philosophical Naturalism: Clarifying the Connection,” Philo 3, no. 2 (Fall–Winter 2000): 7–29, along with Michael Martin’s “Justifying Methodological Naturalism,” both found at www.infidels.org/library.]

I myself have written a few things about it. Now for a few new thoughts.

Methodological naturalism is the backbone of science. We cannot have science without it. To see this, just think of the extreme position where every question is settled by saying “only God knows,” or “the Bible says it; We believe it, that settles it.”

The question of naturalism only arises when it comes to the gaps in our knowledge. Why does it only apply to the gaps? There are many thousands of scientific experiments taking place every single day. In previous centuries those experiments would’ve been testing something on the cutting edges of the science of that day. But because the science of today is considered normal science (ala Thomas Kuhn) Christian defenders don’t raise the question of methodological naturalism about them.

Most early scientists were Christians and they used this method in order to discover the facts about the world. Ronald L. Numbers tells us:

"By the late Middle Ages the search for natural causes had come to typify the work of Christian natural philosophers. Although characteristically leaving the door open for the possibility of direct divine intervention, they frequently expressed contempt for soft-minded contemporaries who invoked miracles rather than searching for natural explanations. The University of Paris cleric Jean Buridan (a. 1295-ca. 1358), described as “perhaps the most brilliant arts master of the Middle Ages,” contrasted the philosopher’s search for “appropriate natural causes” with the common folk’s erroneous habit of attributing unusual astronomical phenomena to the supernatural. In the fourteenth century the natural philosopher Nicole Oresme (ca. 1320-82), who went on to become a Roman Catholic bishop, admonished that, in discussing various marvels of nature, “there is no reason to take recourse to the heavens, the last refuge of the weak, or demons, or to our glorious God as if He would produce these effects directly, more so than those effects whose causes we believe are well known to us.

Enthusiasm for the naturalistic study of nature picked up in the sixteenth and seventeenth centuries as more and more Christians turned their attention to discovering the so-called secondary causes that God employed in operating the world. The Italian Catholic Galileo Galilei (1564-1642), one of the foremost promoters of the new philosophy, insisted that nature “never violates the terms of the laws imposed upon her. [Ronald L. Numbers, 2003. “Science without God: Natural Laws and Christian Beliefs.” In: When Science and Christianity Meet, edited by David C. Lindberg, Ronald L. Numbers. Chicago: University Of Chicago Press, pp , p. 267)].

Why would God create a world where scientists must adopt such a method in order for us to discover the facts of science, which would in turn eventually lead them to think the only causes that exist are natural ones, that supernatural explanations are unnecessary?

Even with methodological naturalism God could still overcome it with sufficient objective evidence. The problem is that the evidence doesn’t exist. Christian defenders refuse to admit this. [Just think of the failed repeated attempts to test prayer]. So what they’re actually doing is saving the appearances of their faith. They're tacitly admitting there isn’t sufficient evidence to believe. If it existed they would be crowing about it. They would be the ones touting the virtues of methodological naturalism in science. They would be the ones using it to show sufficient objective evidence exists for their faith.

This point is extremely important for to see. Just think if there existed sufficient objective evidence to overcome the method of naturalism and it's clear this is what they are doing. Their problem is that this kind of evidence does not exist, and it should. So in order to maintain their faith, Christian defenders have to complain about it even though scientists have amassed a massive amount of knowledge from using it, knowledge that changed our world. It's knowledge gained about things that were once on the cutting edges of science, about things that, if Christians defenders were alive in a previous era, they would've complained how methodological naturalism doesn't leave room for faith, in those very areas where science rolled over faith-based thinking.